The production of agricultural goods and in particular food and feed production, in sufficient quantity and quality is an increasingly challenging task. One the one hand, there is a continuous growth of the demand for agricultural products, due to increase in world population as well as increase in the average standard of living for large parts of the world population. On the other hand, the area suitable or available for agriculture is continuously shrinking, partly because of changing climate conditions which can result in deterioration of areas previously suitable for agriculture. A continuous demand exists to increase the yield potential of agricultural crops, or at least maintaining such yield potential when growing agricultural crops under suboptimal or adverse abiotic conditions.
Up to now, efforts to increase the intrinsic yield potential have mainly focused on exploiting the genetic variability within the crops. By traditional breeding techniques existing or induced variant alleles are shuffled into new combinations. More recently, the pool of variability has been expanded through molecular techniques allowing the exchange of genetic material across species, and even kingdom, barriers.
However, much less attention has been devoted to the role epigenetic control mechanisms may play in determining quantitative traits such as yield. Indeed, all quantitative traits such as size and weights in animals or yield, particularly seed yield in crops exhibit variability with a normal distribution, even within a population of genetically identical individuals. Underlying the observed phenotypic variability are genetic components, environmental factors but also epigenetic components. The importance in plants of epigenetic control components in short and long term adaptation to stress has been documented (Molinier et al. 2006, Transgeneration memory of stress in plants. Nature 442, 1046-1049). Furthermore, it has been demonstrated that altered epigenetic states can be transmitted to successive generations that have not been or are no longer exposed to the inducing trigger (also reviewed in Jablonka and Raz, 2009 Transgenerational epigenetic inheritance: prevalence, mechanisms, and implications for the study of heredity and evolution. The Quarterly Review of Biology 84, No. 2, 131-176).
Various parameters have been employed to establish a correlation with the yield potential of a plant. A positive correlation has been found between yield potential and lower cellular respiration rates. Wilson described the response to selection of dark respiration rate of mature leaves in Lolium perenne and its effects on growth of young plants and simulated swards. (Wilson Ann. Bot. 49, 303-312 (1982)). Wilson and Jones described the effect of selection for dark respiration rate of mature leaves on crop yields of Lolium perenne cv. S23. (Wilson and Jones Ann. Bot. 49, 313-320 (1982)). Kraus et al. reported on the yield advantage of a ‘slow-’over a ‘fast-’respiring population of Lolium perenne cv. S23 which depends on plant density. (Kraus et al. New Phytol. 123, 39-44 (1993)) and on the effect of handling on the yield of two populations of Lolium perenne selected for differences in mature leaf respiration rate (Kraus et al. Physiol. Plant. 89, 341-346 (1993)). Nunes-Nesi et al. described enhanced photosynthetic performance and growth as a consequence of decreasing mitochondrial malate dehydrogenase activity in transgenic tomato plants. (Nunes-Nesi et al. Plant Physiol. 137, 611-622 (2005)). Juczczuk et al. reported on the effect of mitochondrial genome rearrangement on respiratory activity, photosynthesis, photorespiration and energy status of MSC16 cucumber (Cucumis sativus) mutant. (Juczczuk et al, Physiol. Plant. 131, 527-541 (2007)).
De Block and De Brouwer described a simple and robust in vitro assay to quantify the vigour of oilseed rape lines and hybrids. (Plant Physiol. Biochem. 40, 845-852 (2002)). WO02/066972 provides methods and means for determining parent inbred plant lines with good combining ability, for determining good combinations of parent inbred plant lines capable of yielding hybrid lines with high heterosis, and further for determining the agronomical performance of different plant lines, which can be performed in vitro by determining the electron flow in the mitochondria under control and stress conditions.
U.S. Pat. No. 6,444,469 describes methods of increasing or decreasing the rate of development of a plant by either increasing or decreasing the amount of methylated DNA found in the plant. The invention further provides plants that have been altered such that their rate of maturation is either increased or decreased relative to the rate of maturation of a non-altered plant.
Lira-Medeiros et al. (PLoS One, 2010 Apr. 26; 5(4):e10326) disclose that individuals with similar genetic profiles presented divergent epigenetic profiles that were characteristic of the population in a particular environment. It was found that of two morphologically different but genetically similar populations of mangrove plants from two different habitats, the population growing near a salt march displayed a hypomethylation of their genomic DNA when compared to plants growing at a riverside.
Boyko et al., (PLoS One. 2010 Mar. 3; 5(3):e9514) show that exposure of Arabidopsis plants to stresses, including salt, UVC, cold, heat and flood, resulted in a higher homologous recombination frequency, increased global genome methylation, and higher tolerance to stress in the untreated progeny. This transgenerational effect did not, however, persist in successive generations. Treatment of the progeny of stressed plants with 5-azacytidine was shown to decrease global genomic methylation and enhance stress tolerance.
Hauben et al. (2009, Proc Natl Acad Sci USA., 106: p 20109-14.), demonstrated that, starting from an isogenic canola population, it was possible to generate through recurrent selection populations with distinct physiological and agronomical characteristics such as yield, energy use efficiency and abiotic stress tolerance, and that those populations were genetically identical but epigenetically different. It was furthermore found that both the DNA methylation patterns as well as the agronomical and physiological characteristics of the selected lines were heritable and that hybrids derived from parent lines selected for high energy use efficiencies had a 5% yield increase on top of heterosis. But although each of the selected lines was characterized by a specific epigenetic profile (histone modifications and global DNA methylation), taken together, the epigenetic characteristics did not reflect the physiological properties of the lines.
Thus, none of the prior art documents describe that specific epigenetic profiles can be linked to particular agronomical characteristics such as energy use efficiency, yield and tolerance to adverse abiotic conditions. The present invention discloses that particular changes in DNA methylation status during development correlate to the plant's vigor and gene expression and as such these features can be used to select (sub)populations of plants which have a higher yield potential and tolerance to adverse abiotic conditions. This problem is solved as herein after described in the different embodiments, examples and claims.